Test mcp

.Rbuildignore

@@ -28,4 +28,6 @@
 
 ^_quarto\.yml$
 ^\.quarto$
+^\.vscode$
 ^\.devcontainer$
+^DEVELOPMENT\.md$

.devcontainer/devcontainer.json

@@ -1,39 +1,55 @@
 {
-  "name": "serodynamics R Development",
-  "build": {
-    "dockerfile": "Dockerfile"
-  },
+  "name": "serodynamics R Package Development",
+  "image": "rocker/tidyverse:latest",
 
-  // Features to add to the dev container
   "features": {
-    "ghcr.io/devcontainers/features/git:1": {}
+    "ghcr.io/devcontainers/features/git:1": {},
+    "ghcr.io/devcontainers/features/github-cli:1": {},
+    "ghcr.io/devcontainers/features/node:1": {
+      "version": "lts"
+    }
   },
-
-  // Configure tool-specific properties
+
   "customizations": {
     "vscode": {
-      "extensions": [
-        "REditorSupport.r",
-        "GitHub.copilot"
-      ],
       "settings": {
         "r.rterm.linux": "/usr/local/bin/R",
-        "r.rpath.linux": "/usr/local/bin/R"
-      }
+        "r.rpath.linux": "/usr/local/bin/R",
+        "terminal.integrated.defaultProfile.linux": "bash"
+      },
+      "extensions": [
+        "rdebugger.r-debugger",
+        "reditorsupport.r",
+        "github.copilot",
+        "github.copilot-chat",
+        "quarto.quarto",
+        "redhat.vscode-yaml",
+        "yzhang.markdown-all-in-one",
+        "streetsidesoftware.code-spell-checker",
+        "eamodio.gitlens"
+      ]
     }
   },
-
-  // Use 'postCreateCommand' to run commands after the container is created
+
   "postCreateCommand": "bash .devcontainer/setup.sh",
-
-  // Set the default shell
+
   "remoteUser": "rstudio",
 
-  // Forward ports for RStudio Server (optional)
   "forwardPorts": [8787],
 
-  // Persist command history across container rebuilds
+  "portsAttributes": {
+    "8787": {
+      "label": "RStudio Server",
+      "onAutoForward": "notify"
+    }
+  },
+
   "mounts": [
-    "source=serodynamics-bashhistory,target=/commandhistory,type=volume"
-  ]
+    "source=${localWorkspaceFolder}/.Rprofile,target=/home/rstudio/.Rprofile,type=bind,consistency=cached"
+  ],
+
+  "containerEnv": {
+    "GITHUB_TOKEN": "${localEnv:GITHUB_TOKEN}",
+    "TZ": "UTC"
+  }
 }

.devcontainer/setup.sh

@@ -1,21 +1,63 @@
 #!/bin/bash
-# Post-creation setup script for the serodynamics dev container
-
-set -e  # Exit on error
+set -e
 
 echo "Setting up serodynamics development environment..."
 
-# Set up persistent bash history
-echo "Configuring bash history persistence..."
-mkdir -p /commandhistory
-touch /commandhistory/.bash_history
-ln -sf /commandhistory/.bash_history /home/rstudio/.bash_history
+# Update package list
+echo "Updating package list..."
+apt-get update
+
+# Install JAGS (required for serodynamics)
+echo "Installing JAGS..."
+apt-get install -y jags
+
+# Install system dependencies for R packages
+echo "Installing system dependencies..."
+apt-get install -y \
+  libcurl4-openssl-dev \
+  libssl-dev \
+  libxml2-dev \
+  libfontconfig1-dev \
+  libharfbuzz-dev \
+  libfribidi-dev \
+  libfreetype6-dev \
+  libpng-dev \
+  libtiff5-dev \
+  libjpeg-dev \
+  libgit2-dev
+
+# Install Quarto
+echo "Installing Quarto..."
+QUARTO_VERSION="1.6.40"  # Updated to latest stable version (January 2026)
+wget -q https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb
+dpkg -i quarto-${QUARTO_VERSION}-linux-amd64.deb
+rm quarto-${QUARTO_VERSION}-linux-amd64.deb
+
+# Install R packages needed for development
+echo "Installing R development packages..."
+Rscript -e "install.packages(c('devtools', 'roxygen2', 'testthat', 'lintr', 'spelling', 'covr', 'rcmdcheck', 'pak'), repos = 'https://cloud.r-project.org')"
+
+# Install rjags from source (required for JAGS interface)
+echo "Installing rjags..."
+Rscript -e "install.packages('rjags', repos = 'https://cloud.r-project.org', type = 'source')"
+
+# Install package dependencies
+echo "Installing package dependencies..."
+Rscript -e "pak::local_install_dev_deps(dependencies = TRUE)"
+
+# Verify JAGS installation
+echo "Verifying JAGS installation..."
+Rscript -e "library(rjags); library(runjags); runjags::testjags()"
 
-# Install project-specific R dependencies
-echo "Installing R package dependencies..."
-if ! Rscript -e 'devtools::install_dev_deps(dependencies = TRUE)'; then
-    echo "Error: Failed to install R dependencies. Please check the output above for details."
-    exit 1
-fi
+# Clean up
+echo "Cleaning up..."
+apt-get clean
+rm -rf /var/lib/apt/lists/*
 
-echo "Setup complete! The environment is ready for development."
+echo "Development environment setup complete!"
+echo ""
+echo "You can now:"
+echo "  - Run 'devtools::load_all()' to load the package"
+echo "  - Run 'devtools::test()' to run tests"
+echo "  - Run 'devtools::check()' to check the package"
+echo "  - Use VS Code tasks (Ctrl+Shift+P -> Tasks: Run Task)"

.github/copilot-instructions.md

@@ -10,6 +10,53 @@
 - **Key Dependencies**: runjags, rjags, JAGS 4.3.1, serocalculator, ggmcmc, dplyr, ggplot2
 - **Lifecycle**: Experimental (under active development)
 
+## Development Environment Options
+
+The repository provides multiple ways to set up your development environment:
+
+### Option 1: Dev Container (Recommended for consistency)
+
+Use the preconfigured development container for a fully automated setup:
+
+1. Install Docker Desktop and VS Code with Dev Containers extension
+2. Open the repository in VS Code
+3. Click "Reopen in Container" when prompted
+4. All dependencies (R, JAGS, system libraries) are installed automatically
+
+See `.devcontainer/README.md` for details.
+
+### Option 2: Local Installation (Traditional)
+
+Install R, JAGS, and dependencies directly on your system (see Critical Setup Requirements below).
+
+### Option 3: GitHub Codespaces
+
+Use the dev container configuration in a cloud environment:
+1. Go to the repository on GitHub
+2. Click "Code" → "Codespaces" → "Create codespace"
+3. Development environment is ready in your browser
+
+## Model Context Protocol (MCP) Integration
+
+The repository includes MCP server configurations in `.github/mcp/mcp-config.json` for enhanced AI-assisted development:
+
+- **Filesystem Server**: Navigate and edit repository files
+- **GitHub Server**: Check CI/CD status, review PRs, manage issues
+- **Git Server**: Version control operations (status, diff, commit, branch)
+- **Brave Search Server**: Look up R documentation and CRAN resources
+
+These servers enhance GitHub Copilot and other AI assistants with context-aware capabilities. See `.github/mcp/README.md` for setup instructions.
+
+## VS Code Configuration
+
+The `.vscode/` directory contains optimized settings for R package development:
+
+- **settings.json**: R-specific editor settings, file associations, and Copilot configuration
+- **extensions.json**: Recommended VS Code extensions for R development
+- **tasks.json**: Quick tasks for common operations (document, test, check, lint)
+
+Use tasks via `Ctrl+Shift+P` → "Tasks: Run Task" or the Command Palette.
+
 ## Critical Setup Requirements
 
 ### Copilot Setup Workflow (Automatic Environment Configuration)
@@ -125,7 +172,7 @@ The package requires R version 4.1.0 or higher. Install R for your platform:
   # Add CRAN repository for latest R version
   sudo apt-get update
   sudo apt-get install -y software-properties-common dirmngr
-  wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/maruti.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+  wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
   sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
   sudo apt-get update
   sudo apt-get install -y r-base r-base-dev
@@ -408,6 +455,21 @@ Team members can trigger actions by commenting on PRs:
 - **pkgdown/**: pkgdown website configuration
   - `_pkgdown.yml`: Site structure, reference organization
 
+- **.github/**: GitHub configuration and workflows
+  - `.github/workflows/`: CI/CD workflow definitions
+  - `.github/mcp/`: Model Context Protocol server configurations
+  - `.github/copilot-instructions.md`: Custom instructions for GitHub Copilot
+
+- **.vscode/**: VS Code workspace configuration
+  - `settings.json`: Editor settings for R development
+  - `extensions.json`: Recommended VS Code extensions
+  - `tasks.json`: Quick tasks for common R package operations
+
+- **.devcontainer/**: Development container configuration
+  - `devcontainer.json`: Container specification and VS Code integration
+  - `setup.sh`: Automated environment setup script
+  - `README.md`: Dev container usage documentation
+
 ### Configuration Files
 
 - **DESCRIPTION**: Package metadata, dependencies, version (0.0.0.9044)

.github/mcp/README.md

@@ -0,0 +1,128 @@
+# Model Context Protocol (MCP) Configuration
+
+This directory contains the MCP server configuration for the serodynamics R package development environment.
+
+## What is MCP?
+
+Model Context Protocol (MCP) is an open protocol that enables seamless integration between AI assistants and development tools. It allows AI assistants to interact with your development environment through standardized servers.
+
+## Configured MCP Servers
+
+The `mcp-config.json` file configures the following MCP servers:
+
+### 1. Filesystem Server
+- **Purpose**: Provides file system access to the repository
+- **Use cases**: Reading/writing files, searching code, managing project structure
+- **Scope**: `/home/runner/work/serodynamics/serodynamics`
+
+### 2. GitHub Server
+- **Purpose**: Integrates with GitHub for repository operations
+- **Use cases**: Issue tracking, pull requests, workflow management, CI/CD status
+- **Authentication**: Uses `GITHUB_TOKEN` environment variable
+
+### 3. Git Server
+- **Purpose**: Provides Git version control operations
+- **Use cases**: Status checks, diff viewing, log inspection, commits, branch management
+- **Scope**: Repository at `/home/runner/work/serodynamics/serodynamics`
+
+### 4. Brave Search Server
+- **Purpose**: Enables web search capabilities
+- **Use cases**: Finding R package documentation, CRAN resources, troubleshooting
+- **Authentication**: Uses `BRAVE_API_KEY` environment variable (optional)
+
+## Setup Instructions
+
+### Important: Update Repository Paths
+
+**Before using this configuration**, you must update the hardcoded repository paths in `mcp-config.json` to match your local clone location:
+
+1. Open `.github/mcp/mcp-config.json`
+2. Find all instances of `/home/runner/work/serodynamics/serodynamics`
+3. Replace with your local repository path, for example:
+   - macOS/Linux: `/Users/yourname/projects/serodynamics` or `/home/yourname/serodynamics`
+   - Windows: `C:\\Users\\yourname\\projects\\serodynamics`
+
+The default paths are specific to GitHub Actions CI environment and will not work for local development.
+
+### Prerequisites
+
+1. **Node.js**: Required to run the MCP servers via `npx`
+   ```bash
+   # Check if Node.js is installed
+   node --version
+   npm --version
+   ```
+
+2. **Environment Variables**:
+   - `GITHUB_TOKEN`: GitHub Personal Access Token (required for GitHub server)
+   - `BRAVE_API_KEY`: Brave Search API key (optional, for web search)
+
+### Using with GitHub Copilot
+
+1. **In VS Code**:
+   - Install the latest GitHub Copilot extension
+   - The MCP configuration will be automatically detected from `.github/mcp/mcp-config.json`
+   - Copilot will use these servers to enhance code suggestions and operations
+
+2. **In JetBrains IDEs**:
+   - Install GitHub Copilot plugin
+   - Configure MCP servers through the Copilot settings
+   - Point to this `mcp-config.json` file
+
+### Using with Claude Desktop
+
+If you want to use these MCP servers with Claude Desktop:
+
+1. Copy the `mcpServers` section from `mcp-config.json`
+2. **Update the repository paths** (`/home/runner/work/serodynamics/serodynamics`) to your local clone path
+3. Add the modified configuration to your Claude Desktop configuration file:
+   - **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
+   - **Windows**: `%APPDATA%\Claude\claude_desktop_config.json`
+   - **Linux**: `~/.config/Claude/claude_desktop_config.json`
+
+## Development Workflow Integration
+
+The MCP servers are particularly useful for:
+
+1. **Code Navigation**: Quickly finding and reading R source files
+2. **Testing**: Checking test results and coverage
+3. **CI/CD**: Monitoring workflow status and debugging failures
+4. **Documentation**: Finding R package documentation and CRAN resources
+5. **Version Control**: Managing commits, branches, and reviewing changes
+
+## Best Practices
+
+1. **Always check Git status** before making commits using the Git MCP server
+2. **Use the GitHub server** to monitor CI/CD workflows and PR status
+3. **Leverage filesystem search** to find similar code patterns in the repository
+4. **Search the web** for R package documentation when implementing new features
+
+## Troubleshooting
+
+### MCP servers not starting
+
+1. Ensure Node.js is installed and `npx` is available
+2. Check that environment variables are set correctly
+3. Verify repository paths are correct for your system
+
+### GitHub authentication issues
+
+1. Ensure `GITHUB_TOKEN` is set with appropriate scopes:
+   - `repo` (full control of private repositories)
+   - `workflow` (update GitHub Action workflows)
+   - `read:org` (read org and team membership)
+
+2. Generate a new token at: https://github.com/settings/tokens
+
+### Permission issues
+
+1. Ensure the filesystem server has read/write access to the repository
+2. Check that you have the necessary GitHub repository permissions
+
+## References
+
+- [MCP Specification](https://modelcontextprotocol.io/)
+- [MCP Filesystem Server](https://github.com/modelcontextprotocol/servers/tree/main/src/filesystem)
+- [MCP GitHub Server](https://github.com/modelcontextprotocol/servers/tree/main/src/github)
+- [MCP Git Server](https://github.com/modelcontextprotocol/servers/tree/main/src/git)
+- [GitHub Copilot Documentation](https://docs.github.com/en/copilot)